Collection of SARS-CoV-2 Virus from the Air of a Clinic within a University Student Health Care Center and Analyses of the Viral Genomic Sequence

Lednicky, John A.; Shankar, Sripriya Nannu; Elbadry, Maha A.; Gibson, Julia C.; Alam, Md. Mahbubul; Stephenson, Caroline J.; Eiguren-Fernandez, Arantzazu; Morris, J. Glenn; Mavian, Carla; Salemi, Marco; Clugston, James R.; Wu, Chang‐Yu

doi:10.4209/aaqr.2020.02.0202

Cited by 73 publications

(67 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The vRNAs served as templates to construct a cDNA library using an NEBNext Ultra RNA Library Prep Kit (New England BioLabs ® Inc.) followed by sequencing on an Illumina MiSeq sequencer using a version 3 chemistry 600 cycle kit. The complete genome sequence of SARS-CoV-2 in the environmental sample (designated as UF-11) was determined using a genome walking strategy [ 10 ]. Briefly, cDNA was produced using AccuScript high-fidelity reverse transcriptase (Agilent Technologies, Santa Clara, CA) and sequence-specific primers based on SARS-CoV-2 WIV04 (GenBank MN996528.1).…”

Section: Methodsmentioning

confidence: 99%

Earliest detection to date of SARS-CoV-2 in Florida: Identification together with influenza virus on the main entry door of a university building, February 2020

et al. 2021

Self Cite

View full text Add to dashboard Cite

In February and March, 2020, environmental surface swab samples were collected from the handle of the main entry door of a major university building in Florida, as part of a pilot surveillance project screening for influenza. Samples were taken at the end of regular classroom hours, between the dates of February 1–5 and February 19-March 4, 2020. Influenza A(H1N1)pdm09 virus was isolated from the door handle on four of the 19 days sampled. Both SARS-CoV-2 and A(H1N1)pdm09 virus were detected in a sample collected on February 21, 2020. Based on sequence analysis, the Florida SARS-CoV-2 strain (designated UF-11) was identical to strains being identified in Washington state during the same time period, while the earliest similar sequences were sampled in China/Hubei between Dec 30th 2019 and Jan 5th 2020. The first human case of COVID-19 was not officially reported in Florida until March 1st. In an analysis of sequences from COVID-19 patients in this region of Florida, there was only limited evidence of subsequent dissemination of the UF-11 strain. Identical or highly similar strains, possibly related through a common transmission chain, were detected with increasing frequency in Washington state between end of February and beginning of March. Our data provide further documentation of the rapid early spread of SARS-CoV-2 and underscore the likelihood that closely related strains were cryptically circulating in multiple U.S. communities before the first “official” cases were recognized.

show abstract

Section: Methodsmentioning

confidence: 99%

Earliest detection to date of SARS-CoV-2 in Florida: Identification together with influenza virus on the main entry door of a university building, February 2020

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…3 Conversely, numerous researchers [4][5][6][7][8][9][10][11][12] and professional societies (e.g., ASHRAE 13 ) have raised concerns that longer-range airborne transmission is likely occurring from both symptomatic and asymptomatic (or pre-symptomatic) individuals through a combination of larger respiratory droplets that are carried further than 1-2 m via airflow patterns and smaller inhalable aerosols (i.e., 'droplet nuclei') that can easily transport over longer distances. These concerns arise from a growing understanding of human respiratory emissions, 14,15 known transmission pathways of other respiratory viruses, 16 recent empirical evidence detecting SARS-CoV-2 in aerosol and surface samples in healthcare settings, [17][18][19][20] and recent case studies demonstrating the likely importance of longer-range aerosol transmission in some settings. 21,22 Understanding the importance of each transmission pathway for COVID-19 is critical to informing public health guidelines for effectively managing the spread of the disease.…”

Section: Introductionmentioning

confidence: 99%

Mechanistic Transmission Modeling of COVID-19 on the Diamond Princess Cruise Ship Demonstrates the Importance of Aerosol Transmission

Azimi

Keshavarz

Laurent

et al. 2020

Preprint

View full text Add to dashboard Cite

Background The current prevailing position is that coronavirus disease 2019 (COVID-19) is transmitted primarily through large respiratory droplets within close proximity (i.e., 1-2 m) of infected individuals. However, quantitative information on the relative importance of specific transmission pathways of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (i.e., droplets, aerosols, and fomites across short- and long-range distances) remains limited. Methods To evaluate the relative importance of multiple transmission routes for SARS-CoV-2, we leveraged detailed information available from the Diamond Princess Cruise Ship outbreak that occurred in early 2020. We developed a framework that combines stochastic Markov chain and negative exponential dose-response modeling with available empirical data on mechanisms of SARS-CoV-2 dynamics and human behaviors, which informs a modified version of the Reed-Frost epidemic model to predict daily and cumulative daily case counts on the ship. We modeled 21,600 scenarios to generate a matrix of solutions across a full range of assumptions for eight unknown or uncertain epidemic and mechanistic transmission factors, including the magnitude of droplet and aerosol emissions from infected individuals, the infectious dose for deposition of droplets and aerosols to the upper and lower respiratory tracts, and others. Findings A total of 132 model iterations met acceptability criteria (R2 > 0.95 for modeled vs. reported cumulative daily cases and R2 > 0 for daily cases). Analyzing only these successful model iterations yields insights into the likely values for uncertain parameters and quantifies the likely contributions of each defined mode of transmission. Mean estimates of the contributions of short-range, long-range, and fomite transmission modes to infected cases aboard the ship across the entire simulation time period were 35%, 35%, and 30%, respectively. Mean estimates of the contributions of large respiratory droplets and small respiratory aerosols were 41% and 59%. Short-range transmission was the dominant mode after passenger quarantine began, albeit due primarily to aerosol transmission, not droplets. Interpretation Our results demonstrate that aerosol inhalation was likely the dominant contributor to COVID-19 transmission among passengers aboard the Diamond Princess Cruise Ship. Moreover, close-range and long-range transmission likely contributed similarly to disease progression aboard the ship, with fomite transmission playing a smaller role. The passenger quarantine also affected the importance of each mode, demonstrating the impacts of the interventions. Although cruise ships represent unique built environments with high ventilation rates and no air recirculation, these findings underscore the importance of implementing public health measures that target the control of inhalation of aerosols in addition to ongoing measures targeting control of large droplet and fomite transmission, not only aboard cruise ships but in other indoor environments as well.

show abstract

“…The robustness of amplicon-sequencing to degraded and low concentrations of RNA is evident from studies of environmental specimens, where this approach is followed by sequencing with Ion torrent [ 62 ] or ONT [ 63 ] for wastewater samples, and by Sanger sequencing for a patient breathing air sample and for a door handle swab ([ 64 ] and J.A.Lednicky, personal communication).…”

Section: High-throughput Sequencing For Covid-19 Pandemicmentioning

confidence: 99%

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

Chiara

D’Erchia

Gissi

et al. 2020

Briefings in Bioinformatics

192

153

View full text Add to dashboard Cite

Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic. Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes. We also present an outline of current repositories and databases that provide access to SARS-CoV-2 genomic data and associated metadata. Finally, we offer general advice and guidelines for the appropriate sharing and deposition of SARS-CoV-2 data and metadata, and suggest that more efficient and standardized integration of current and future SARS-CoV-2-related data would greatly facilitate the struggle against this new pathogen. We hope that our ‘ vademecum ’ for the production and handling of SARS-CoV-2-related sequencing data, will contribute to this objective.

show abstract

Collection of SARS-CoV-2 Virus from the Air of a Clinic within a University Student Health Care Center and Analyses of the Viral Genomic Sequence

Cited by 73 publications

References 22 publications

Earliest detection to date of SARS-CoV-2 in Florida: Identification together with influenza virus on the main entry door of a university building, February 2020

Earliest detection to date of SARS-CoV-2 in Florida: Identification together with influenza virus on the main entry door of a university building, February 2020

Mechanistic Transmission Modeling of COVID-19 on the Diamond Princess Cruise Ship Demonstrates the Importance of Aerosol Transmission

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

Contact Info

Product

Resources

About